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haplo.stats (version 1.7.9)

Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous

Description

Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.

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Version

Install

install.packages('haplo.stats')

Monthly Downloads

1,909

Version

1.7.9

License

GPL (>= 2)

Maintainer

Jason Sinnwell

Last Published

April 11th, 2018

Functions in haplo.stats (1.7.9)

geno.count.pairs

Counts of Total Haplotype Pairs Produced by Genotypes

Get a list of objects for haplotype pairs

Set of haplotypes and frequencies for power and sample size calculations

Integer Rank Codes for Haplotypes

Search for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window

haplo.em.fitter

Compute engine for haplotype EM algorithm

summary.haplo.glm

Print and summary of a haplo.glm object

anova.haplo.glm

Analysis of variance for haplo.glm model fit

Compute Generalized Inverse of Input Matrix

GLM Regression of Trait on Ambiguous Haplotypes

haplo.model.frame

Sets up a model frame for haplo.glm

haplo.score.merge

Merge haplo.score And haplo.group Objects

Score Statistics for Association of Traits with Haplotypes

haplo.score.slide

Score Statistics for Association of Traits with Haplotypes

Print contents of a haplo.em object

find.haplo.beta.qt

Find beta coefficients for risk haplotypes, for specified r2

print.haplo.scan

Print a haplo.scan object

print.haplo.group

Print a haplo.group object

fitted.haplo.glm

Fitted values from haplo.glm fit

Power and sample size for the chi-square distribution

Print a nice banner

Build a design matrix for haplotypes

Haplotype Association Analysis in a Case-Control design

Power and sample size for the F distribution

Frequencies for Haplotypes by Grouping Variable

haplo.glm.control

Create list of control parameters for haplo.glm

print.haplo.score

Print a haplo.score object

residuals.haplo.glm

Accessing residuals for haplo.glm fit

Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions.

HLA Loci and Serologic Response to Measles Vaccination

Find Location from Mouse Clicks and Print Haplotypes on Plot

Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class.

Creates an object of class "locus"

plot.haplo.score

Plot Haplotype Frequencies versus Haplotype Score Statistics

Simulated data for seqhap examples

Louis Information for haplo.glm

plot.haplo.score.slide

Plot a haplo.score.slide Object

score.sim.control

Create the list of control parameters for simulations in haplo.score

consistency checks for x.linked locus

Remove rows with NA in covariates, but keep genotypes with NAs

Sequential Haplotype Scan Association Analysis for Case-Control Data

print.haplo.score.merge

Print a haplo.score.merge object

print.haplo.score.slide

Print the contents of a haplo.score.slide object

Summarize Full Haplotype Enumeration on Genotype Matrix

variance-covariance matrix of a fitted haplo.glm object

Plot a seqhap object

Print a haplo.cc object

summary.haplo.em

Summarize contents of a haplo.em object

convert genotype matrix from 1-column 2-column

EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci

haplo.em.control

Create the Control Parameters for the EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci

Compute either power or sample size for haplotype associations with a quantitative trait.

Compute either power or sample size for haplotype associations in a case-control study.